Starting phenix.real_space_refine on Sat Jul 4 00:12:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8flw_29288/07_2026/8flw_29288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flw_29288/07_2026/8flw_29288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8flw_29288/07_2026/8flw_29288.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8flw_29288/07_2026/8flw_29288.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8flw_29288/07_2026/8flw_29288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flw_29288/07_2026/8flw_29288.map" model { file = "/net/cci-nas-00/data/ceres_data/8flw_29288/07_2026/8flw_29288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flw_29288/07_2026/8flw_29288.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 10497 2.51 5 N 2809 2.21 5 O 3443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16868 Number of models: 1 Model: "" Number of chains: 37 Chain: "H" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "A" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "B" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.37, per 1000 atoms: 0.20 Number of scatterers: 16868 At special positions: 0 Unit cell: (132.126, 128.877, 175.446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 3443 8.00 N 2809 7.00 C 10497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.07 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.08 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN N 4 " - " MAN N 5 " " MAN Q 4 " - " MAN Q 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA E 3 " - " MAN E 6 " " BMA N 3 " - " MAN N 6 " " BMA Q 3 " - " MAN Q 6 " " BMA X 3 " - " MAN X 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG D 1 " - " ASN C 197 " " NAG E 1 " - " ASN C 262 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 332 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 234 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 332 " " NAG I 606 " - " ASN I 339 " " NAG I 607 " - " ASN I 355 " " NAG I 608 " - " ASN I 392 " " NAG I 609 " - " ASN I 137 " " NAG J 1 " - " ASN C 295 " " NAG K 1 " - " ASN C 363 " " NAG M 1 " - " ASN C 386 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 276 " " NAG P 1 " - " ASN G 197 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 276 " " NAG S 1 " - " ASN G 295 " " NAG T 1 " - " ASN G 363 " " NAG U 1 " - " ASN G 386 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN I 197 " " NAG X 1 " - " ASN I 262 " " NAG Y 1 " - " ASN I 276 " " NAG Z 1 " - " ASN I 295 " " NAG a 1 " - " ASN I 363 " " NAG b 1 " - " ASN I 386 " " NAG c 1 " - " ASN I 448 " " NAG d 1 " - " ASN I 160 " " NAG e 1 " - " ASN I 156 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 620.2 milliseconds 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 33 sheets defined 23.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'H' and resid 27 through 32 removed outlier: 3.573A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 62 Processing helix chain 'H' and resid 73 through 76 removed outlier: 4.009A pdb=" N SER H 76 " --> pdb=" O SER H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 73 through 76' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.914A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.307A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.674A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.690A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.516A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.064A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.645A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.645A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.717A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.104A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.381A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.547A pdb=" N TRP C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.575A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.656A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.240A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.607A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.819A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.644A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.538A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 64 removed outlier: 4.076A pdb=" N GLU G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 58 through 64' Processing helix chain 'G' and resid 98 through 116 removed outlier: 4.186A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 354 removed outlier: 4.008A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 390 removed outlier: 3.640A pdb=" N LEU G 390 " --> pdb=" O THR G 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 387 through 390' Processing helix chain 'G' and resid 476 through 484 removed outlier: 3.522A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.322A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.774A pdb=" N LEU I 125 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 122 through 126' Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 350 removed outlier: 3.799A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR I 341 " --> pdb=" O THR I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 476 through 484 removed outlier: 4.351A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 removed outlier: 4.052A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR H 68 " --> pdb=" O GLU H 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.963A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA H 88 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 39 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP H 50 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY H 56 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.963A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA H 88 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 39 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS H 35 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR H 94 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU H 105 " --> pdb=" O THR H 94 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER H 96 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 100E removed outlier: 6.687A pdb=" N GLU H 100O" --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE H 100D" --> pdb=" O TYR H 100M" (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR H 100M" --> pdb=" O PHE H 100D" (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.939A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.934A pdb=" N HIS L 53 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS L 49 " --> pdb=" O HIS L 53 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.697A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 603 through 609 removed outlier: 4.644A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.992A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.886A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.476A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AB5, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.654A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 374 through 377 removed outlier: 3.641A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 302 through 308 removed outlier: 6.780A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 603 through 609 removed outlier: 7.384A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.205A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 55 through 56 Processing sheet with id=AC2, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.225A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.573A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.487A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.643A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.487A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 302 through 309 removed outlier: 6.921A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AC8, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.594A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD1, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.012A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AD3, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.739A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 271 through 273 removed outlier: 4.303A pdb=" N THR I 467 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.696A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 305 through 309 removed outlier: 3.696A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2655 1.29 - 1.43: 4464 1.43 - 1.56: 9910 1.56 - 1.70: 2 1.70 - 1.83: 157 Bond restraints: 17188 Sorted by residual: bond pdb=" C MET I 161 " pdb=" O MET I 161 " ideal model delta sigma weight residual 1.234 1.160 0.074 1.28e-02 6.10e+03 3.30e+01 bond pdb=" C PRO C 124 " pdb=" O PRO C 124 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.20e-02 6.94e+03 2.88e+01 bond pdb=" CA ALA C 319 " pdb=" CB ALA C 319 " ideal model delta sigma weight residual 1.535 1.457 0.079 1.71e-02 3.42e+03 2.12e+01 bond pdb=" OH TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.679 1.590 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" N PRO C 124 " pdb=" CA PRO C 124 " ideal model delta sigma weight residual 1.468 1.423 0.045 1.10e-02 8.26e+03 1.67e+01 ... (remaining 17183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 22671 2.37 - 4.75: 560 4.75 - 7.12: 95 7.12 - 9.50: 5 9.50 - 11.87: 2 Bond angle restraints: 23333 Sorted by residual: angle pdb=" C THR C 320 " pdb=" CA THR C 320 " pdb=" CB THR C 320 " ideal model delta sigma weight residual 110.19 98.32 11.87 1.64e+00 3.72e-01 5.24e+01 angle pdb=" CA MET I 161 " pdb=" C MET I 161 " pdb=" O MET I 161 " ideal model delta sigma weight residual 121.58 113.61 7.97 1.16e+00 7.43e-01 4.72e+01 angle pdb=" C ASN C 262 " pdb=" CA ASN C 262 " pdb=" CB ASN C 262 " ideal model delta sigma weight residual 111.89 120.76 -8.87 1.42e+00 4.96e-01 3.90e+01 angle pdb=" CA ASN C 262 " pdb=" CB ASN C 262 " pdb=" CG ASN C 262 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 angle pdb=" C TYS H 100F" pdb=" CA TYS H 100F" pdb=" CB TYS H 100F" ideal model delta sigma weight residual 110.10 99.40 10.70 1.90e+00 2.77e-01 3.17e+01 ... (remaining 23328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8583 18.00 - 35.99: 749 35.99 - 53.99: 168 53.99 - 71.98: 33 71.98 - 89.98: 17 Dihedral angle restraints: 9550 sinusoidal: 3872 harmonic: 5678 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 165.49 -72.49 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -147.39 61.39 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -146.06 60.06 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 9547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2884 0.156 - 0.312: 36 0.312 - 0.467: 2 0.467 - 0.623: 0 0.623 - 0.779: 1 Chirality restraints: 2923 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 MAN E 5 " pdb=" O2 MAN E 4 " pdb=" C2 MAN E 5 " pdb=" O5 MAN E 5 " both_signs ideal model delta sigma weight residual False 2.40 2.60 -0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.68e+01 ... (remaining 2920 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.257 2.00e-02 2.50e+03 2.20e-01 6.03e+02 pdb=" C7 NAG E 1 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.368 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.103 2.00e-02 2.50e+03 8.54e-02 9.12e+01 pdb=" C7 NAG O 2 " 0.025 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.139 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 427 " 0.023 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C TRP C 427 " -0.082 2.00e-02 2.50e+03 pdb=" O TRP C 427 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN C 428 " 0.028 2.00e-02 2.50e+03 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 17 2.29 - 2.95: 8043 2.95 - 3.60: 21806 3.60 - 4.25: 35738 4.25 - 4.90: 60534 Nonbonded interactions: 126138 Sorted by model distance: nonbonded pdb=" OG SER C 447 " pdb=" C1 NAG E 1 " model vdw 1.644 3.470 nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.084 3.040 nonbonded pdb=" O THR C 123 " pdb=" OG1 THR C 123 " model vdw 2.113 3.040 nonbonded pdb=" OG1 THR A 627 " pdb=" OE1 GLN A 630 " model vdw 2.174 3.040 nonbonded pdb=" O SER C 460 " pdb=" OG1 THR C 461 " model vdw 2.181 3.040 ... (remaining 126133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 33 through 609) selection = (chain 'G' and resid 33 through 609) selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.040 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17327 Z= 0.293 Angle : 0.859 25.802 23713 Z= 0.431 Chirality : 0.056 0.779 2923 Planarity : 0.006 0.220 2834 Dihedral : 14.310 89.978 5767 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.45 % Favored : 95.29 % Rotamer: Outliers : 0.81 % Allowed : 0.64 % Favored : 98.56 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1931 helix: 1.40 (0.31), residues: 336 sheet: -0.01 (0.23), residues: 557 loop : -0.38 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 166 TYR 0.010 0.001 TYR H 100M PHE 0.011 0.001 PHE I 53 TRP 0.022 0.001 TRP C 427 HIS 0.004 0.000 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.29 (17188) covalent geometry : angle 0.80133 / 0.42 (23333) SS BOND : bond 0.01096 / 0.76 ( 37) SS BOND : angle 1.75997 / 1.04 ( 74) hydrogen bonds : bond 0.27390 / 18.36 ( 493) hydrogen bonds : angle 8.29132 / 5.55 ( 1329) link_ALPHA1-2 : bond 0.00312 / 0.16 ( 4) link_ALPHA1-2 : angle 3.71685 / 2.17 ( 12) link_ALPHA1-3 : bond 0.00447 / 0.23 ( 4) link_ALPHA1-3 : angle 2.05453 / 1.24 ( 12) link_ALPHA1-6 : bond 0.00924 / 0.48 ( 4) link_ALPHA1-6 : angle 3.09126 / 1.80 ( 12) link_BETA1-4 : bond 0.00379 / 0.22 ( 32) link_BETA1-4 : angle 2.06021 / 1.30 ( 96) link_NAG-ASN : bond 0.01268 / 1.01 ( 58) link_NAG-ASN : angle 2.98049 / 2.21 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 371 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.6359 (ppp) cc_final: 0.6074 (ppp) REVERT: L 32 TYR cc_start: 0.7241 (m-80) cc_final: 0.6618 (m-80) REVERT: A 579 ARG cc_start: 0.8921 (mtp180) cc_final: 0.8608 (mtm180) REVERT: A 586 TYR cc_start: 0.8989 (t80) cc_final: 0.8745 (t80) REVERT: A 601 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7949 (mttp) REVERT: B 638 TYR cc_start: 0.5916 (m-80) cc_final: 0.5709 (m-80) REVERT: C 153 GLU cc_start: 0.6960 (tp30) cc_final: 0.6613 (tp30) REVERT: F 591 GLN cc_start: 0.7896 (tt0) cc_final: 0.7653 (tt0) REVERT: G 111 LEU cc_start: 0.8966 (mt) cc_final: 0.8735 (mt) REVERT: G 112 TRP cc_start: 0.8009 (t-100) cc_final: 0.7685 (t-100) REVERT: I 35 TRP cc_start: 0.7819 (m100) cc_final: 0.7541 (m100) REVERT: I 38 VAL cc_start: 0.9091 (p) cc_final: 0.8805 (m) REVERT: I 104 MET cc_start: 0.8408 (ttt) cc_final: 0.8203 (ttt) REVERT: I 217 TYR cc_start: 0.8252 (m-80) cc_final: 0.8035 (m-80) REVERT: I 475 MET cc_start: 0.8495 (tpp) cc_final: 0.8084 (tpp) outliers start: 14 outliers final: 6 residues processed: 381 average time/residue: 0.1153 time to fit residues: 66.0078 Evaluate side-chains 216 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 205 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN L 93 HIS A 543 ASN B 543 ASN B 625 ASN C 103 GLN C 105 HIS C 185 ASN C 195 ASN C 203 GLN F 630 GLN G 99 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN G 280 ASN I 114 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.173924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141261 restraints weight = 23474.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143020 restraints weight = 18231.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144994 restraints weight = 15028.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145274 restraints weight = 13210.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.145366 restraints weight = 12314.979| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17327 Z= 0.162 Angle : 0.743 25.080 23713 Z= 0.343 Chirality : 0.047 0.365 2923 Planarity : 0.004 0.034 2834 Dihedral : 4.413 43.140 2112 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.19 % Allowed : 9.76 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1931 helix: 1.38 (0.29), residues: 342 sheet: 0.20 (0.23), residues: 528 loop : -0.47 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.023 0.002 TYR H 91 PHE 0.022 0.002 PHE C 53 TRP 0.016 0.001 TRP A 631 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (17188) covalent geometry : angle 0.66925 / 0.33 (23333) SS BOND : bond 0.00520 / 0.36 ( 37) SS BOND : angle 1.43166 / 1.11 ( 74) hydrogen bonds : bond 0.06736 / 4.64 ( 493) hydrogen bonds : angle 5.95020 / 3.97 ( 1329) link_ALPHA1-2 : bond 0.00372 / 0.19 ( 4) link_ALPHA1-2 : angle 1.99506 / 1.25 ( 12) link_ALPHA1-3 : bond 0.00745 / 0.37 ( 4) link_ALPHA1-3 : angle 1.33728 / 0.83 ( 12) link_ALPHA1-6 : bond 0.00519 / 0.26 ( 4) link_ALPHA1-6 : angle 1.71049 / 1.07 ( 12) link_BETA1-4 : bond 0.00473 / 0.28 ( 32) link_BETA1-4 : angle 1.45124 / 0.97 ( 96) link_NAG-ASN : bond 0.00484 / 0.29 ( 58) link_NAG-ASN : angle 3.53722 / 2.93 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 MET cc_start: 0.5091 (mpp) cc_final: 0.4717 (mpp) REVERT: L 32 TYR cc_start: 0.7855 (m-80) cc_final: 0.7586 (m-80) REVERT: A 542 ARG cc_start: 0.8320 (ttp-170) cc_final: 0.8091 (ttp-170) REVERT: A 601 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7939 (mttp) REVERT: C 153 GLU cc_start: 0.7381 (tp30) cc_final: 0.7003 (tp30) REVERT: C 198 THR cc_start: 0.9245 (m) cc_final: 0.8931 (p) REVERT: F 571 TRP cc_start: 0.8144 (m100) cc_final: 0.7863 (m100) REVERT: G 111 LEU cc_start: 0.8941 (mt) cc_final: 0.8726 (mt) REVERT: G 112 TRP cc_start: 0.8128 (t-100) cc_final: 0.7721 (t-100) REVERT: I 38 VAL cc_start: 0.9111 (p) cc_final: 0.8873 (m) REVERT: I 428 GLN cc_start: 0.8131 (mp10) cc_final: 0.7904 (mt0) REVERT: I 475 MET cc_start: 0.8379 (tpp) cc_final: 0.8036 (tpp) outliers start: 38 outliers final: 24 residues processed: 260 average time/residue: 0.1098 time to fit residues: 44.3248 Evaluate side-chains 226 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 186 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 177 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN L 90 GLN L 93 HIS F 591 GLN F 640 GLN G 99 ASN G 249 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.168526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135327 restraints weight = 23930.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137115 restraints weight = 17927.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.139890 restraints weight = 14582.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140569 restraints weight = 11666.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140825 restraints weight = 10640.590| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17327 Z= 0.179 Angle : 0.689 15.904 23713 Z= 0.319 Chirality : 0.047 0.386 2923 Planarity : 0.003 0.043 2834 Dihedral : 4.353 34.949 2101 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.41 % Allowed : 11.84 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1931 helix: 0.64 (0.28), residues: 378 sheet: 0.12 (0.23), residues: 545 loop : -0.42 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 585 TYR 0.021 0.002 TYR A 586 PHE 0.022 0.002 PHE C 53 TRP 0.015 0.002 TRP H 108 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (17188) covalent geometry : angle 0.64183 / 0.31 (23333) SS BOND : bond 0.00381 / 0.24 ( 37) SS BOND : angle 1.08978 / 0.81 ( 74) hydrogen bonds : bond 0.05115 / 3.53 ( 493) hydrogen bonds : angle 5.27984 / 3.52 ( 1329) link_ALPHA1-2 : bond 0.00317 / 0.16 ( 4) link_ALPHA1-2 : angle 1.73910 / 1.10 ( 12) link_ALPHA1-3 : bond 0.00544 / 0.27 ( 4) link_ALPHA1-3 : angle 1.30758 / 0.80 ( 12) link_ALPHA1-6 : bond 0.00384 / 0.19 ( 4) link_ALPHA1-6 : angle 1.51816 / 0.95 ( 12) link_BETA1-4 : bond 0.00468 / 0.31 ( 32) link_BETA1-4 : angle 1.41579 / 0.93 ( 96) link_NAG-ASN : bond 0.00520 / 0.32 ( 58) link_NAG-ASN : angle 2.69642 / 2.04 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 222 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 GLN cc_start: 0.5308 (tt0) cc_final: 0.4956 (tt0) REVERT: H 100 PHE cc_start: 0.8570 (p90) cc_final: 0.8235 (p90) REVERT: L 31 ASN cc_start: 0.8469 (p0) cc_final: 0.8166 (p0) REVERT: A 542 ARG cc_start: 0.8444 (ttp-170) cc_final: 0.8177 (ttp-170) REVERT: A 601 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8153 (mtmm) REVERT: A 615 SER cc_start: 0.8659 (t) cc_final: 0.8357 (m) REVERT: C 153 GLU cc_start: 0.7507 (tp30) cc_final: 0.7037 (tp30) REVERT: F 520 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7527 (pt) REVERT: F 626 MET cc_start: 0.8086 (ttm) cc_final: 0.7874 (ttm) REVERT: G 475 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7361 (ptm) REVERT: I 38 VAL cc_start: 0.9231 (p) cc_final: 0.8966 (m) REVERT: I 475 MET cc_start: 0.8298 (tpp) cc_final: 0.8014 (tpp) outliers start: 59 outliers final: 38 residues processed: 261 average time/residue: 0.1072 time to fit residues: 44.2986 Evaluate side-chains 239 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 93 optimal weight: 5.9990 chunk 101 optimal weight: 0.0870 chunk 67 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 179 optimal weight: 0.9990 chunk 184 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 93 HIS C 374 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.171331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138942 restraints weight = 23554.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141119 restraints weight = 16289.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143608 restraints weight = 13606.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143844 restraints weight = 11593.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143992 restraints weight = 10699.711| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17327 Z= 0.108 Angle : 0.625 12.640 23713 Z= 0.288 Chirality : 0.045 0.362 2923 Planarity : 0.003 0.028 2834 Dihedral : 4.109 27.925 2101 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.89 % Allowed : 13.97 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1931 helix: 0.91 (0.28), residues: 378 sheet: 0.20 (0.23), residues: 553 loop : -0.37 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 617 TYR 0.015 0.001 TYR I 173 PHE 0.017 0.001 PHE C 53 TRP 0.010 0.001 TRP G 338 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (17188) covalent geometry : angle 0.58037 / 0.28 (23333) SS BOND : bond 0.00263 / 0.13 ( 37) SS BOND : angle 0.81014 / 0.60 ( 74) hydrogen bonds : bond 0.04136 / 2.87 ( 493) hydrogen bonds : angle 4.88966 / 3.24 ( 1329) link_ALPHA1-2 : bond 0.00329 / 0.16 ( 4) link_ALPHA1-2 : angle 1.59195 / 1.02 ( 12) link_ALPHA1-3 : bond 0.00646 / 0.32 ( 4) link_ALPHA1-3 : angle 1.28147 / 0.83 ( 12) link_ALPHA1-6 : bond 0.00405 / 0.20 ( 4) link_ALPHA1-6 : angle 1.43961 / 0.91 ( 12) link_BETA1-4 : bond 0.00422 / 0.27 ( 32) link_BETA1-4 : angle 1.38661 / 0.92 ( 96) link_NAG-ASN : bond 0.00423 / 0.28 ( 58) link_NAG-ASN : angle 2.52462 / 1.89 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8540 (p90) cc_final: 0.8216 (p90) REVERT: L 31 ASN cc_start: 0.8285 (p0) cc_final: 0.8044 (p0) REVERT: L 32 TYR cc_start: 0.7938 (m-80) cc_final: 0.7542 (m-80) REVERT: A 542 ARG cc_start: 0.8457 (ttp-170) cc_final: 0.8250 (ttp-170) REVERT: A 601 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7940 (mttp) REVERT: A 615 SER cc_start: 0.8356 (t) cc_final: 0.8102 (m) REVERT: F 520 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7593 (pt) REVERT: G 111 LEU cc_start: 0.8814 (mt) cc_final: 0.8603 (mt) REVERT: G 475 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7068 (ptm) REVERT: I 38 VAL cc_start: 0.9149 (p) cc_final: 0.8882 (m) outliers start: 50 outliers final: 30 residues processed: 252 average time/residue: 0.1142 time to fit residues: 44.6426 Evaluate side-chains 236 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 160 optimal weight: 0.0060 chunk 23 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN L 90 GLN F 640 GLN G 85 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.168398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136590 restraints weight = 23753.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138524 restraints weight = 18223.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139855 restraints weight = 15700.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140547 restraints weight = 13054.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140726 restraints weight = 12166.190| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17327 Z= 0.144 Angle : 0.659 13.208 23713 Z= 0.303 Chirality : 0.046 0.378 2923 Planarity : 0.003 0.025 2834 Dihedral : 4.143 26.662 2101 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.83 % Allowed : 15.88 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1931 helix: 0.87 (0.28), residues: 378 sheet: 0.10 (0.22), residues: 549 loop : -0.51 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.013 0.001 TYR I 173 PHE 0.016 0.001 PHE C 53 TRP 0.010 0.001 TRP G 112 HIS 0.005 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (17188) covalent geometry : angle 0.61130 / 0.29 (23333) SS BOND : bond 0.00329 / 0.21 ( 37) SS BOND : angle 1.89014 / 1.39 ( 74) hydrogen bonds : bond 0.04189 / 2.89 ( 493) hydrogen bonds : angle 4.84557 / 3.23 ( 1329) link_ALPHA1-2 : bond 0.00276 / 0.14 ( 4) link_ALPHA1-2 : angle 1.62571 / 1.03 ( 12) link_ALPHA1-3 : bond 0.00619 / 0.31 ( 4) link_ALPHA1-3 : angle 1.31922 / 0.82 ( 12) link_ALPHA1-6 : bond 0.00350 / 0.17 ( 4) link_ALPHA1-6 : angle 1.46956 / 0.92 ( 12) link_BETA1-4 : bond 0.00428 / 0.27 ( 32) link_BETA1-4 : angle 1.35236 / 0.89 ( 96) link_NAG-ASN : bond 0.00407 / 0.27 ( 58) link_NAG-ASN : angle 2.46349 / 1.82 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8584 (p90) cc_final: 0.8259 (p90) REVERT: L 90 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7017 (pp30) REVERT: A 601 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8112 (mtmm) REVERT: A 615 SER cc_start: 0.8414 (t) cc_final: 0.8164 (m) REVERT: F 540 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: F 621 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7076 (tm-30) REVERT: G 217 TYR cc_start: 0.7975 (m-80) cc_final: 0.7082 (m-80) REVERT: G 475 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7021 (ptm) REVERT: I 38 VAL cc_start: 0.9250 (p) cc_final: 0.8980 (m) outliers start: 49 outliers final: 32 residues processed: 248 average time/residue: 0.1114 time to fit residues: 42.9942 Evaluate side-chains 244 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 122 optimal weight: 0.0770 chunk 169 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN F 640 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.167878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135528 restraints weight = 23572.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136993 restraints weight = 17190.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139562 restraints weight = 14343.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.140003 restraints weight = 12238.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140175 restraints weight = 10881.964| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17327 Z= 0.137 Angle : 0.649 14.586 23713 Z= 0.298 Chirality : 0.046 0.382 2923 Planarity : 0.003 0.034 2834 Dihedral : 4.153 27.868 2100 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.66 % Allowed : 16.63 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1931 helix: 0.64 (0.28), residues: 396 sheet: 0.09 (0.22), residues: 549 loop : -0.54 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.019 0.001 TYR A 586 PHE 0.015 0.001 PHE C 53 TRP 0.010 0.001 TRP B 596 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (17188) covalent geometry : angle 0.60538 / 0.29 (23333) SS BOND : bond 0.00290 / 0.17 ( 37) SS BOND : angle 1.55058 / 1.17 ( 74) hydrogen bonds : bond 0.04053 / 2.78 ( 493) hydrogen bonds : angle 4.77731 / 3.18 ( 1329) link_ALPHA1-2 : bond 0.00281 / 0.14 ( 4) link_ALPHA1-2 : angle 1.60621 / 1.02 ( 12) link_ALPHA1-3 : bond 0.00562 / 0.28 ( 4) link_ALPHA1-3 : angle 1.31223 / 0.82 ( 12) link_ALPHA1-6 : bond 0.00340 / 0.17 ( 4) link_ALPHA1-6 : angle 1.45923 / 0.91 ( 12) link_BETA1-4 : bond 0.00417 / 0.26 ( 32) link_BETA1-4 : angle 1.36478 / 0.90 ( 96) link_NAG-ASN : bond 0.00391 / 0.26 ( 58) link_NAG-ASN : angle 2.38537 / 1.75 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 90 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.6971 (pp30) REVERT: A 542 ARG cc_start: 0.8418 (ttp-170) cc_final: 0.8145 (ttp-170) REVERT: A 601 LYS cc_start: 0.8539 (mtpt) cc_final: 0.7974 (mttp) REVERT: A 615 SER cc_start: 0.8458 (t) cc_final: 0.8231 (m) REVERT: B 648 GLU cc_start: 0.7416 (pp20) cc_final: 0.7134 (pp20) REVERT: F 540 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: G 114 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7931 (tm-30) REVERT: G 217 TYR cc_start: 0.8032 (m-80) cc_final: 0.7100 (m-80) REVERT: G 475 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7085 (ptm) REVERT: I 38 VAL cc_start: 0.9231 (p) cc_final: 0.8968 (m) REVERT: I 474 ASP cc_start: 0.6080 (t0) cc_final: 0.5851 (t0) outliers start: 46 outliers final: 34 residues processed: 242 average time/residue: 0.1132 time to fit residues: 43.0500 Evaluate side-chains 243 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN F 640 GLN I 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.164027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.130594 restraints weight = 23950.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132307 restraints weight = 17600.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134367 restraints weight = 15011.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.134979 restraints weight = 12448.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135804 restraints weight = 11279.962| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17327 Z= 0.255 Angle : 0.761 15.053 23713 Z= 0.352 Chirality : 0.049 0.432 2923 Planarity : 0.004 0.062 2834 Dihedral : 4.635 27.317 2100 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.18 % Allowed : 16.57 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1931 helix: 0.34 (0.28), residues: 396 sheet: -0.06 (0.23), residues: 525 loop : -0.78 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 38 TYR 0.023 0.002 TYR A 586 PHE 0.016 0.002 PHE C 383 TRP 0.013 0.002 TRP G 112 HIS 0.007 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.25 (17188) covalent geometry : angle 0.71673 / 0.34 (23333) SS BOND : bond 0.00437 / 0.30 ( 37) SS BOND : angle 1.84110 / 1.35 ( 74) hydrogen bonds : bond 0.04854 / 3.34 ( 493) hydrogen bonds : angle 5.07150 / 3.40 ( 1329) link_ALPHA1-2 : bond 0.00215 / 0.11 ( 4) link_ALPHA1-2 : angle 1.80443 / 1.12 ( 12) link_ALPHA1-3 : bond 0.00524 / 0.26 ( 4) link_ALPHA1-3 : angle 1.50928 / 0.87 ( 12) link_ALPHA1-6 : bond 0.00332 / 0.17 ( 4) link_ALPHA1-6 : angle 1.62361 / 0.99 ( 12) link_BETA1-4 : bond 0.00443 / 0.28 ( 32) link_BETA1-4 : angle 1.46696 / 0.96 ( 96) link_NAG-ASN : bond 0.00474 / 0.31 ( 58) link_NAG-ASN : angle 2.61688 / 1.90 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 31 ASN cc_start: 0.8322 (p0) cc_final: 0.8063 (p0) REVERT: A 542 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.8126 (ttp-170) REVERT: A 601 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8265 (mtmm) REVERT: A 615 SER cc_start: 0.8540 (t) cc_final: 0.8295 (m) REVERT: F 540 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: F 648 GLU cc_start: 0.7219 (pm20) cc_final: 0.7007 (pm20) REVERT: G 456 ARG cc_start: 0.8393 (ptm-80) cc_final: 0.8169 (tmm-80) REVERT: G 475 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7129 (ptm) REVERT: I 38 VAL cc_start: 0.9185 (p) cc_final: 0.8918 (m) outliers start: 55 outliers final: 41 residues processed: 238 average time/residue: 0.1318 time to fit residues: 48.7152 Evaluate side-chains 230 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 134 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 110 HIS L 90 GLN C 99 ASN C 103 GLN F 630 GLN F 640 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.163644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.130879 restraints weight = 23935.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132720 restraints weight = 17811.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135176 restraints weight = 14864.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135755 restraints weight = 12085.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.135850 restraints weight = 10927.517| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17327 Z= 0.182 Angle : 0.722 19.885 23713 Z= 0.328 Chirality : 0.048 0.448 2923 Planarity : 0.003 0.066 2834 Dihedral : 4.511 28.621 2100 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.94 % Allowed : 17.49 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 1931 helix: 0.42 (0.28), residues: 396 sheet: -0.07 (0.22), residues: 535 loop : -0.76 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 617 TYR 0.019 0.002 TYR A 586 PHE 0.016 0.002 PHE C 53 TRP 0.011 0.001 TRP G 69 HIS 0.005 0.001 HIS H 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (17188) covalent geometry : angle 0.66797 / 0.31 (23333) SS BOND : bond 0.00285 / 0.15 ( 37) SS BOND : angle 1.60544 / 1.19 ( 74) hydrogen bonds : bond 0.04315 / 2.98 ( 493) hydrogen bonds : angle 4.89870 / 3.26 ( 1329) link_ALPHA1-2 : bond 0.00250 / 0.13 ( 4) link_ALPHA1-2 : angle 1.71788 / 1.06 ( 12) link_ALPHA1-3 : bond 0.00568 / 0.29 ( 4) link_ALPHA1-3 : angle 1.42150 / 0.86 ( 12) link_ALPHA1-6 : bond 0.00303 / 0.15 ( 4) link_ALPHA1-6 : angle 1.52364 / 0.95 ( 12) link_BETA1-4 : bond 0.00409 / 0.26 ( 32) link_BETA1-4 : angle 1.44034 / 0.94 ( 96) link_NAG-ASN : bond 0.00622 / 0.38 ( 58) link_NAG-ASN : angle 2.91807 / 2.11 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 31 ASN cc_start: 0.8310 (p0) cc_final: 0.8054 (p0) REVERT: L 90 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7200 (pp30) REVERT: A 542 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.8138 (ttp-170) REVERT: A 601 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8261 (mtmm) REVERT: F 540 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: F 621 GLU cc_start: 0.7608 (tm-30) cc_final: 0.6985 (tm-30) REVERT: G 456 ARG cc_start: 0.8396 (ptm-80) cc_final: 0.8080 (tmm-80) REVERT: G 475 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7138 (ptm) REVERT: I 38 VAL cc_start: 0.9090 (p) cc_final: 0.8869 (m) outliers start: 51 outliers final: 38 residues processed: 231 average time/residue: 0.1265 time to fit residues: 45.9205 Evaluate side-chains 229 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 58 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN F 630 GLN F 640 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.164508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131934 restraints weight = 23738.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133886 restraints weight = 17794.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135522 restraints weight = 14622.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135989 restraints weight = 12806.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136059 restraints weight = 11860.810| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17327 Z= 0.142 Angle : 0.689 17.669 23713 Z= 0.314 Chirality : 0.047 0.509 2923 Planarity : 0.004 0.094 2834 Dihedral : 4.426 29.698 2100 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.37 % Allowed : 18.42 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1931 helix: 0.47 (0.28), residues: 396 sheet: 0.06 (0.23), residues: 513 loop : -0.80 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100A TYR 0.018 0.001 TYR A 586 PHE 0.015 0.001 PHE C 53 TRP 0.011 0.001 TRP G 338 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (17188) covalent geometry : angle 0.63971 / 0.30 (23333) SS BOND : bond 0.00268 / 0.14 ( 37) SS BOND : angle 1.46883 / 1.09 ( 74) hydrogen bonds : bond 0.04062 / 2.80 ( 493) hydrogen bonds : angle 4.79048 / 3.19 ( 1329) link_ALPHA1-2 : bond 0.00266 / 0.13 ( 4) link_ALPHA1-2 : angle 1.66571 / 1.03 ( 12) link_ALPHA1-3 : bond 0.00581 / 0.29 ( 4) link_ALPHA1-3 : angle 1.38506 / 0.85 ( 12) link_ALPHA1-6 : bond 0.00319 / 0.16 ( 4) link_ALPHA1-6 : angle 1.48468 / 0.92 ( 12) link_BETA1-4 : bond 0.00409 / 0.26 ( 32) link_BETA1-4 : angle 1.40922 / 0.92 ( 96) link_NAG-ASN : bond 0.00530 / 0.33 ( 58) link_NAG-ASN : angle 2.69138 / 1.95 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 MET cc_start: 0.5353 (mpp) cc_final: 0.5081 (mpp) REVERT: L 31 ASN cc_start: 0.8363 (p0) cc_final: 0.8082 (p0) REVERT: L 90 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7056 (pp30) REVERT: A 542 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8162 (ttp-170) REVERT: A 601 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8213 (mtmm) REVERT: F 540 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: G 475 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7032 (ptm) REVERT: I 38 VAL cc_start: 0.9109 (p) cc_final: 0.8869 (m) outliers start: 41 outliers final: 35 residues processed: 225 average time/residue: 0.1280 time to fit residues: 44.9523 Evaluate side-chains 228 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 186 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 193 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN F 630 GLN F 640 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.163102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131370 restraints weight = 23791.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132954 restraints weight = 18689.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135335 restraints weight = 15435.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.135491 restraints weight = 12902.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135684 restraints weight = 12123.764| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17327 Z= 0.187 Angle : 0.711 17.020 23713 Z= 0.326 Chirality : 0.048 0.475 2923 Planarity : 0.003 0.053 2834 Dihedral : 4.488 29.628 2100 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.54 % Allowed : 18.48 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 1931 helix: 0.40 (0.28), residues: 396 sheet: -0.05 (0.22), residues: 531 loop : -0.80 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.019 0.002 TYR A 586 PHE 0.015 0.002 PHE C 53 TRP 0.025 0.001 TRP C 69 HIS 0.005 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (17188) covalent geometry : angle 0.66503 / 0.31 (23333) SS BOND : bond 0.00293 / 0.15 ( 37) SS BOND : angle 1.62121 / 1.17 ( 74) hydrogen bonds : bond 0.04224 / 2.91 ( 493) hydrogen bonds : angle 4.83401 / 3.22 ( 1329) link_ALPHA1-2 : bond 0.00259 / 0.13 ( 4) link_ALPHA1-2 : angle 1.70116 / 1.04 ( 12) link_ALPHA1-3 : bond 0.00551 / 0.28 ( 4) link_ALPHA1-3 : angle 1.43342 / 0.86 ( 12) link_ALPHA1-6 : bond 0.00291 / 0.14 ( 4) link_ALPHA1-6 : angle 1.54551 / 0.95 ( 12) link_BETA1-4 : bond 0.00425 / 0.27 ( 32) link_BETA1-4 : angle 1.42427 / 0.93 ( 96) link_NAG-ASN : bond 0.00544 / 0.34 ( 58) link_NAG-ASN : angle 2.60452 / 1.88 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: L 31 ASN cc_start: 0.8357 (p0) cc_final: 0.8112 (p0) REVERT: L 90 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7402 (pp30) REVERT: A 542 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8164 (ttp-170) REVERT: A 601 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8236 (mtmm) REVERT: F 540 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: F 621 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7243 (tm-30) REVERT: G 475 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7020 (ptm) REVERT: I 38 VAL cc_start: 0.9120 (p) cc_final: 0.8870 (m) outliers start: 44 outliers final: 39 residues processed: 225 average time/residue: 0.1297 time to fit residues: 45.7873 Evaluate side-chains 231 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 54 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN C 99 ASN C 103 GLN F 630 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.163197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.129813 restraints weight = 23809.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132353 restraints weight = 18045.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135120 restraints weight = 13837.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.135357 restraints weight = 11842.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135448 restraints weight = 10898.246| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17327 Z= 0.174 Angle : 0.703 16.975 23713 Z= 0.323 Chirality : 0.047 0.438 2923 Planarity : 0.004 0.074 2834 Dihedral : 4.490 30.259 2100 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.77 % Allowed : 18.30 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1931 helix: 0.41 (0.28), residues: 396 sheet: -0.05 (0.22), residues: 529 loop : -0.82 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.018 0.002 TYR A 586 PHE 0.015 0.002 PHE C 53 TRP 0.028 0.001 TRP C 69 HIS 0.005 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (17188) covalent geometry : angle 0.65909 / 0.31 (23333) SS BOND : bond 0.00289 / 0.15 ( 37) SS BOND : angle 1.55032 / 1.13 ( 74) hydrogen bonds : bond 0.04164 / 2.87 ( 493) hydrogen bonds : angle 4.81850 / 3.21 ( 1329) link_ALPHA1-2 : bond 0.00263 / 0.13 ( 4) link_ALPHA1-2 : angle 1.69764 / 1.04 ( 12) link_ALPHA1-3 : bond 0.00555 / 0.28 ( 4) link_ALPHA1-3 : angle 1.42686 / 0.86 ( 12) link_ALPHA1-6 : bond 0.00296 / 0.15 ( 4) link_ALPHA1-6 : angle 1.53331 / 0.95 ( 12) link_BETA1-4 : bond 0.00426 / 0.27 ( 32) link_BETA1-4 : angle 1.42761 / 0.93 ( 96) link_NAG-ASN : bond 0.00533 / 0.33 ( 58) link_NAG-ASN : angle 2.55670 / 1.84 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.71 seconds wall clock time: 44 minutes 35.61 seconds (2675.61 seconds total)